Hi,
I have the following code which raises an exception because the molecule
is not up to its expectations. But I can't find a way to trap the
exception. Can someone suggest one, please?
from rdkit import Chem
from rdkit.Chem import AvailDescriptors
from rdkit.Chem import Crippen
m=Chem.MolFromSmiles('c1ccc2c(c1)/C=N/c3ccccc3S[Ti]O2.[CH]1[CH][CH][CH][
CH]1.Cl[Sn-](Cl)(Cl)(Cl)Cl')
# I tried this way
molog = Crippen.MolLogP(m)
print molog
# and also this way first
if AvailDescriptors.descDict['MolLogP'](m):
mollogp = AvailDescriptors.descDict['MolLogP'](m)
I also wanted to calc. NumHDonors and NumHAcceptors. But if it failed on
one descriptor, will it fail on other descriptors as well?
Any suggestions?
Thanks
Sridhar
p.s. to Eddie. Turned out my server has the 11g client and the
installation on the server works fine. I guess I must have missed a line
or two of instructions that the client must be 11g's and not the DB
itself. My PC had oracle 9 and 10 clients.
From: Eddie Cao [mailto:cao.yi...@gmail.com]
Sent: Wednesday, October 20, 2010 4:26 PM
To: Kuntamukkula, Sridhar (Hlthcr&Science)
Cc: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] [Rdkit-devel] How to build the RDKit?
Hi,
Being not an Oracle user, I cannot give you a concrete answer, but a
quick Google search indicates that it might be a version inconsistency
between the client and the server. Are you sure you are connecting to
11g? Please contact your database administrator for problems regarding
Oracle database or ask the folks on the cx_Oracle mailing list:
http://lists.sourceforge.net/lists/listinfo/cx-oracle-users
-Eddie
On Oct 20, 2010, at 11:03 AM, sridhar.kuntamukk...@thomsonreuters.com
wrote:
Hi,
I have downloaded the "Windows x86 Installer
<http://prdownloads.sourceforge.net/cx-oracle/cx_Oracle-5.0.4-11g.win32-
py2.5.msi?download> (Oracle 11g, Python 2.5)" to my PC and installed
it.
>From Python command-line, when I try to connect to oracle, I get the
following error.
C:\RDkit>python
Python 2.5 (r25:51908, Sep 19 2006, 09:52:17) [MSC v.1310 32 bit
(Intel)] on win
32
Type "help", "copyright", "credits" or "license" for more information.
>>> import cx_Oracle
>>> con = cx_Oracle.connect("user", "pwd", "chemdev")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
cx_Oracle.DatabaseError: ORA-24315: illegal attribute type
I have originally used the connstr=user/p...@chemdev' and this gave me
the same error as above.
Then I found the above syntax in the cx_oracle_doc folder's readme.txt
and am lost now.
MY PC has Windows XP, Oracle is on a different server (with a TNS entry
"chemdev") and I just added TNS_ADMIN Registry_entry and the path of
TNS_ADMIN to the PATH env. Variable.
>From a command prompt, sqlplus user/p...@chemdev works fine.
Any thoughts?
Many thanks
Sridhar
From: nikolaus.sti...@novartis.com [mailto:nikolaus.sti...@novartis.com]
Sent: Wednesday, October 20, 2010 2:07 AM
To: Eddie Cao
Cc: rdkit-de...@lists.sourceforge.net; Kuntamukkula, Sridhar
(Hlthcr&Science); rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-devel] How to build the RDKit?
Hi Sridhar,
congrats on getting things working. One more comment - maybe you want to
post these kind of questions rather in the discuss than the devel list.
It is much more populated and you will for sure get replies quicker.
Cheers
Nik
Eddie Cao <cao.yi...@gmail.com>
10/19/2010 11:49 PM
To
sridhar.kuntamukk...@thomsonreuters.com
cc
rdkit-de...@lists.sourceforge.net
Subject
Re: [Rdkit-devel] How to build the RDKit?
Hi Sridhar,
Congratulations! If from rdkit import Chem gives you >>>, then it is
very good sign that things are all in place.
To load molecules from Oracle database, you need a database connector
called cx_Oracle. After installing this module, you will be able to send
SQL statement to Oracle to retrieve molecule SMILES or SDF, depending on
how molecules are stored in your database. You might need to consult
your database administrator.
To download cx_Oracle: http://cx-oracle.sourceforge.net/
For a simple example about how to use it:
http://wiki.oracle.com/page/Python
Check Section 14 of the Getting Started in Python Guide for a complete
list of descriptors you can calculate using RDKit:
http://rdkit.org/GettingStartedInPython.pdf
Regards,
Eddie
On Oct 19, 2010, at 2:31 PM, sridhar.kuntamukk...@thomsonreuters.com
wrote:
Hi Nik,
Looks like I had a version issue with the RDkit I downloaded. I needed
Q22010_1 for Python2.5 but I downloaded Q22009_1 in which, it was
looking for Python2.5 (hardcoded path from one of the libs, looked like)
when I ran the test command (hence I downloaded and installed Python2.5
and removed 2.6).
Now that I have a clean install of Py2.5 and fresh download of RDkit
Q22010_1 for Py2.5, the test command ran well and passed the test.
I just have to go to the next step.
I need to create molLogP, NumHAcceptors, NumHDonors etc.. values for a
given molecule.
My molecules are actually stored in an Oracle DB.
So, Where do I begin?
I just got your other mail. The install is set and OK now as it seems.
I ran the command "from rdkit import Chem" from the command-line and it
put me back to the >>> prompt, no add'l msgs.
As for sending to the whole group, it was an honest mistake. I just
clicked "Reply". Some other lists that I subscribed to, send to the list
automagically. I realized my mistake when I didn't receive the mail back
to me and fixed it in this one.
Regards,
Sridhar
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